CPGP Concept matching calculation with inner product
Created: 2014-05-27 11:49:38
Last updated: 2014-06-30 09:24:31
Part of the CPGP to create concept pairs for calculating the inner product and insert the values into a premade mysql table. This workflow needs to be run after CPGP Contingency table Calculate uncertainty coefficient
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Authors (1)
Titles (1)
| Concept Profile Generation Pipeline |
Descriptions (1)
| Requirements:
Have MySQL installed with a database called mydb or please create one.
Have a mysql connector file. This can be downloaded from mysql.com.
Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab.
Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader.
Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downloads
Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Change lvg.properties
LVG_DIR=/home/path/to/lvg2013lite/
This file can be found in:
/home/path/to/lvg2013lite/data/config/lvg.properties
Copy properties file from production.properties which can be found on: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path.
This file can be obtained from https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Have Peregrine indexer installed locally and give it the correct path in the component named "Indexer_tool". Which can be found in the nested workflow named Peregrine indexer.
If using a Windows machine please install cygwin. Set cygwin in the $PATH of the environment variabale.
Go to taverna File --> preferences --> Tool invocation --> set modify on explicit locations --> edit a default local to Shell: C:\Windows\system32\cmd.exe /c and save that. -->Set Modify on: symbolic locations --> edit --> choose default local and save.
Have JAVA_HOME C:\Program Files\jdk 1.7.0 in environment variabale when using Windows.
The nested workflow Get_abstract uses a sql command to retrieve abstracts which presumes that it uses the mydb database. Please change this when using a other sql database. |
Dependencies (0)
Inputs (1)
| Name |
Description |
| db_properties |
Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated.
|
Processors (3)
| Name |
Type |
Description |
| Calculate Contincengy table |
workflow |
A nested workflow that retrieves the values of a 2x2 contingency table and puts the co-occurence of made concept pairs into the SQL table TableName_co_occurence.
This is done by creating concept pairs which is retrieved from the Sql table TableName_occurence.
This contincengy table consits out of a matrix where two concepts co-occur, concept A only occurs
and not concept B, concept B occurs and not concept A and neither concepts occur in literature.
B Not B
A AB A
not A B not A not B
This is calculated for every possible concept pair. |
| Calculate Inner Product |
workflow |
A nested workflow to calculate the inner product of a concept profile. |
| table_name |
stringconstant |
Valuealpha |
Beanshells (4)
| Name |
Description |
Inputs |
Outputs |
| Beanshell_SQL_generate_Get_Inner_Product |
A Beanshell script that generates a SQL statement to calculate the inner product between two concept profiles.
These concept profiles only have concepts that both have in common. The concepts that are in common in the concept profiles are multiplied with each others UC value and added. This summed up value of two concept profiles is the inner product.
For example:
Concept profile A, has the concept A, B, C and D. Concept profile B has the concepts B, C, E. This means the common concepts for both concept profiles are B, C. Deze waardes worden gemultipliceerd en opgeteld. |
concept_pairs
timestamp
|
out1
|
| Beanshell_SQL_generate_INSERT_INTO_Inner_Product_table |
A Beanshell script that generates a SQL statement to insert the inner product values calculated of two concept profiles into the inner product table. |
concept_pairs
timestamp
inner_product_value
|
out1
|
| Beanshell_generate_SQL_statement_Get_destinct_concept |
A Beanshell script that retrieves every concept from the Sql table TableName_occurence. |
table_name
|
out1
|
| Beanshell_make_concept_pairs |
A Beanshell script that gets as input a list of concepts to create concept pairs. |
concept_B
concept_A
|
concept_pair
|
Datalinks (6)
| Source |
Sink |
| db_properties |
Calculate Contincengy table:propertyString |
| table_name:value |
Calculate Contincengy table:table_name |
| Calculate Contincengy table:outputlist |
Calculate Inner Product:concept_pairs |
| db_properties |
Calculate Inner Product:propertyString |
| table_name:value |
Calculate Inner Product:timestamp |
| Calculate Inner Product:output |
end |
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